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Transcriptome genetics using second generation sequencing in a Caucasian population

Author

Listed:
  • Stephen B. Montgomery

    (University of Geneva Medical School
    Wellcome Trust Sanger Institute)

  • Micha Sammeth

    (Center for Genomic Regulation, University Pompeu Fabra, Barcelona, Catalonia, 08003 Spain)

  • Maria Gutierrez-Arcelus

    (University of Geneva Medical School)

  • Radoslaw P. Lach

    (Wellcome Trust Sanger Institute)

  • Catherine Ingle

    (Wellcome Trust Sanger Institute)

  • James Nisbett

    (Wellcome Trust Sanger Institute)

  • Roderic Guigo

    (Center for Genomic Regulation, University Pompeu Fabra, Barcelona, Catalonia, 08003 Spain)

  • Emmanouil T. Dermitzakis

    (University of Geneva Medical School
    Wellcome Trust Sanger Institute)

Abstract

RNA sequencing unlocks key to gene expression There is currently much interest in the understanding of genetic mechanisms that underlie variation at the gene expression level. Two groups reporting in this issue of Nature use RNA sequencing to study global gene expression in two contrasting populations. Pickrell et al. sequenced RNA from 69 lymphoblastoid cell lines derived from unrelated Nigerian individuals who have been extensively genotyped as part of the HapMap Project. By pooling data from all the individuals it was possible to identify many genetic determinants of variation in gene expression. Montgomery et al. characterize the mRNA fraction of RNA isolated from lymphoblastoid cell lines derived from 63 HapMap individuals of Caucasian origin. They obtain a fine-scale view of the transcriptome and identify genetic variants that affect alternative splicing.

Suggested Citation

  • Stephen B. Montgomery & Micha Sammeth & Maria Gutierrez-Arcelus & Radoslaw P. Lach & Catherine Ingle & James Nisbett & Roderic Guigo & Emmanouil T. Dermitzakis, 2010. "Transcriptome genetics using second generation sequencing in a Caucasian population," Nature, Nature, vol. 464(7289), pages 773-777, April.
    • Handle: RePEc:nat:nature:v:464:y:2010:i:7289:d:10.1038_nature08903
    DOI: 10.1038/nature08903
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    Citations

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    Cited by:

    1. Jean Francois Lefebvre & Emilio Vello & Bing Ge & Stephen B Montgomery & Emmanouil T Dermitzakis & Tomi Pastinen & Damian Labuda, 2012. "Genotype-Based Test in Mapping Cis-Regulatory Variants from Allele-Specific Expression Data," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-15, June.
    2. Farnoosh Abbas-Aghababazadeh & Qian Li & Brooke L Fridley, 2018. "Comparison of normalization approaches for gene expression studies completed with high-throughput sequencing," PLOS ONE, Public Library of Science, vol. 13(10), pages 1-21, October.
    3. Kensuke Yamaguchi & Kazuyoshi Ishigaki & Akari Suzuki & Yumi Tsuchida & Haruka Tsuchiya & Shuji Sumitomo & Yasuo Nagafuchi & Fuyuki Miya & Tatsuhiko Tsunoda & Hirofumi Shoda & Keishi Fujio & Kazuhiko , 2022. "Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    4. Kyung-Won Hong & Seok Won Jeong & Myungguen Chung & Seong Beom Cho, 2014. "Association between Expression Quantitative Trait Loci and Metabolic Traits in Two Korean Populations," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-13, December.
    5. John Platig & Peter J Castaldi & Dawn DeMeo & John Quackenbush, 2016. "Bipartite Community Structure of eQTLs," PLOS Computational Biology, Public Library of Science, vol. 12(9), pages 1-17, September.
    6. Alexandra C Nica & Leopold Parts & Daniel Glass & James Nisbet & Amy Barrett & Magdalena Sekowska & Mary Travers & Simon Potter & Elin Grundberg & Kerrin Small & Åsa K Hedman & Veronique Bataille & Jo, 2011. "The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study," PLOS Genetics, Public Library of Science, vol. 7(2), pages 1-9, February.
    7. Barbara E Stranger & Stephen B Montgomery & Antigone S Dimas & Leopold Parts & Oliver Stegle & Catherine E Ingle & Magda Sekowska & George Davey Smith & David Evans & Maria Gutierrez-Arcelus & Alkes P, 2012. "Patterns of Cis Regulatory Variation in Diverse Human Populations," PLOS Genetics, Public Library of Science, vol. 8(4), pages 1-13, April.
    8. Thanh Nguyen & Asim Bhatti & Samuel Yang & Saeid Nahavandi, 2016. "RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process," PLOS ONE, Public Library of Science, vol. 11(10), pages 1-18, October.
    9. Eric O Johnson & Dana B Hancock & Nathan C Gaddis & Joshua L Levy & Grier Page & Scott P Novak & Cristie Glasheen & Nancy L Saccone & John P Rice & Michael P Moreau & Kimberly F Doheny & Jane M Romm &, 2015. "Novel Genetic Locus Implicated for HIV-1 Acquisition with Putative Regulatory Links to HIV Replication and Infectivity: A Genome-Wide Association Study," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-15, March.
    10. Jungsoo Gim & Sungho Won & Taesung Park, 2016. "LPEseq: Local-Pooled-Error Test for RNA Sequencing Experiments with a Small Number of Replicates," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-15, August.
    11. Daria V Zhernakova & Eleonora de Klerk & Harm-Jan Westra & Anastasios Mastrokolias & Shoaib Amini & Yavuz Ariyurek & Rick Jansen & Brenda W Penninx & Jouke J Hottenga & Gonneke Willemsen & Eco J de Ge, 2013. "DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts," PLOS Genetics, Public Library of Science, vol. 9(6), pages 1-15, June.
    12. Faisal Shahla & Tutz Gerhard, 2017. "Missing value imputation for gene expression data by tailored nearest neighbors," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 16(2), pages 95-106, April.

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